lysA-I

UniProt ID: Q88L58
Organism: Pseudomonas putida KT2440
Review Status: DRAFT
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Gene Description

lysA-I (PP_2077) encodes the PLP-dependent diaminopimelate decarboxylase (DAPDC; EC 4.1.1.20) that converts meso-2,6-diaminopimelate to L-lysine and carbon dioxide in the terminal reaction of the diaminopimelate pathway. KT2440 also encodes the LysA-II protein Q88CF4, and the relative physiological contributions of the two paralogs are unresolved.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: This root catalytic term is redundant with the specific DAPDC activity.
Reason: GO:0008836 identifies the actual substrate-specific reaction.
GO:0008836 diaminopimelate decarboxylase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: This is the defining LysA-I molecular function.
Reason: EC 4.1.1.20, RHEA:15101, HAMAP MF_02120, NCBIfam:TIGR01048, and the LysA-specific InterPro signature support the same decarboxylation. The cited support is the curated HAMAP MF_02120 function statement and the family matches; Q88L58 has not been assayed directly.
Supporting Evidence:
file:PSEPK/lysA-I/lysA-I-uniprot.txt
Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.
file:PSEPK/lysA-I/lysA-I-uniprot.txt
DR NCBIfam; TIGR01048; lysA; 1.
file:PSEPK/lysA-I/lysA-I-uniprot.txt
DR InterPro; IPR002986; DAP_deCOOHase_LysA.
GO:0009085 L-lysine biosynthetic process
IEA
GO_REF:0000002 		ACCEPT
Summary: LysA-I performs the terminal reaction of L-lysine biosynthesis.
Reason: UniProt assigns Q88L58 to L-lysine biosynthesis via the DAP pathway.
GO:0016831 carboxy-lyase activity
IEA
GO_REF:0000117 		MARK AS OVER ANNOTATED
Summary: This broad lyase term is redundant with the specific DAPDC activity.
Reason: GO:0008836 captures the substrate-specific decarboxylation.
GO:0030170 pyridoxal phosphate binding
IEA
GO_REF:0000104 		KEEP AS NON CORE
Summary: PLP binding is valid cofactor context for DAPDC catalysis.
Reason: Cofactor binding is less informative than the substrate-specific reaction.

Core Functions

PLP-dependent decarboxylation of meso-2,6-diaminopimelate to L-lysine in the terminal step of the DAP pathway.

Molecular Function:
diaminopimelate decarboxylase activity
Directly Involved In:
L-lysine biosynthetic process
Supporting Evidence:
  • file:PSEPK/lysA-I/lysA-I-uniprot.txt
    Specifically catalyzes the decarboxylation of meso-
  • file:PSEPK/lysA-I/lysA-I-deep-research-openscientist.md
    Q88L58 (lysA-I / PP_2077) is a PLP-dependent diaminopimelate decarboxylase catalyzing the final step of lysine biosynthesis.

References

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Knowledge Gaps

What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).

Gap: The relative in-vivo flux, conditional expression, and redundancy of the Q88L58 LysA-I and Q88CF4 LysA-II paralogs are unresolved.

BIOLOGY

What is known: Both proteins retain the exact DAP decarboxylase assignment; neither copy has target-specific genetics establishing individual essentiality.

Provenance (the field's own admissions):

Deep Research

OpenScientist

(lysA-I-deep-research-openscientist.md)

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